Reproducibility of size and shape for epitaxially grown self-assembling Mn-based nanostructures was achieved by tracing the formation process via reflectance difference spectroscopy. Pure Mn crystallites were at first fabricated on a CdTe(001) Te-terminated surface and, in a second stage, a variety of well-controlled strain-induced island morphologies was obtained with the deposition of semiconducting materials on the magnetic precursors.